User:Karsten Theis/AI tutorial: Difference between revisions

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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
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Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well).
Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well).
<nowiki>
load files "=3H54" "=3LX9"                                                          # load 2 files, they are selected as 1.1 and 2.1 below
restrict none                                                                      # display is cleared
define ~act2 2.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A    # active site residues of 3LX9
define ~act1 1.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A    # active site residues of 3H54
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE              # superposition (different sequences, so use alpha carbon)
set ssbonds SIDECHAIN                                                              # disulfide bonds are anchored on SG, not on CA
# drawing 3H54 active site
select 1.1 and ~act1 and (sidechain or *.CA); wireframe 60;                        # show the active site as wireframe
color bonds cornflowerblue                                                          # 3H54 is shown in blue (just the bonds)
select selected and not _C; spacefill 80; color cpk                                # spacefill, atoms other than carbon shown using CPK color scheme
select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;
trace 10; color cornflowerblue                                                      # some main chain context for the active site residues
select 1.1 and 1000:A; wireframe 60;                                                # selecting the sugar in 3H54
select selected and _C; color skyblue;                                              # carbons in skyblue
# drawing 3LX9 active site
select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60;                        # show the active site as wireframe
color bonds yellow                                                                  # 3LX9 is shown in yellow (just the bonds)
select selected and not _C; spacefill 80; color cpk                                # spacefill, atoms other than carbon shown using CPK color scheme
select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA;
trace 10; color yellow                                                              # some main chain context for the active site residues
select 2.1 and 1000:A; wireframe 60;;                                              # selecting the sugar in 3LX9
select selected and _C; color beige;                                                # carbons in beige
center selected; zoom 300                                                          # center and zoom in
</nowiki>


===Overall views===
===Overall views===
These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back.
These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back.
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